You'll have to get more responses from some of people that use PrTG but from past posts I believe they normalize their graphs and also do scaling which as far as I know SW's does not ie. the data is more RAW and displayed exactly the way it's polled in Orion. I asume your other concern was that possibly the the polling interval was too tight but you should be able to see how your polling is working by looking at the Polling Engine Status.
Sometimes this can happen if you are using a 32 bit counter to monitor an interface that is pushing a decent amount of traffic. I would suggest checking the box to allow 64 bit counters for the device and see if that clears up the problem.